Scheme - Re: Business Opportunities for SF Bay Lispers?

Author

Re: Business Opportunities for SF Bay Lispers?

Lupo LeBoucher

2004-03-27, 12:24 am

In article <xcvfzcd5emw.fsf@famine.OCF.Berkeley.EDU>,
Thomas F. Burdick <tfb@famine.OCF.Berkeley.EDU> wrote:
>ix@io.com (Lupo LeBoucher) writes:
>
>
>Ha ha ha! Oh, you weren't kidding? Uhm, try adding a bunch of
>biological knowledge to that. The days of being able to get anything
>from a naive/ignorant application of CS to biology are over. We need
>bioinformaticians who are *both* biologists and computer scientists.
>Either one alone won't cut it, at least if you're looking for serious
>progress.

The guys I know who do this sort of thing are all physicists, and they
seem to get a lot of research done without knowing much CS or biology.
They seem to bring a rather different and useful skillset to the plate
than biologists or CS types do. Perhaps because they're used to applying
mathematical ideas to, like, reality.

As for actually making money doing this sort of thing (which is the
subject of this discussion), there is certainly plenty of room for CS
people to do so without knowing a thing about biology, as I have already
pointed out.

-Lupo
'Sex is the mysticism of materialism.'-Malcolm Muggeridge <ix@io.com>

Lupo LeBoucher

2004-03-27, 12:24 am

In article <ouy3c8dv07p.fsf@panix3.panix.com>,
Carl Shapiro <cshapiro+spam@panix.com> wrote:
>ix@io.com (Lupo LeBoucher) writes:
>
> It is unfortunate that an awful lot of what
>
>I would like to challenge you on this point. I have occasionally
>found myself inspecting library code from scripting languages to
>translate back into Lisp.

Well, that's sort of the point:

In Lisp-land you find yourself inspecting library code from scripting
languages to translate back into Lisp. In Python-land, you don't have to
do this.

-Lupo
"They are instructed in excellence in three things from age 5 to 20; to
ride, to draw the bow and to speak the truth." -Herodotus <ix@io.com>

Carl Shapiro

2004-03-27, 12:24 am

ix@io.com (Lupo LeBoucher) writes:

> Well, that's sort of the point:
>
> In Lisp-land you find yourself inspecting library code from scripting
> languages to translate back into Lisp. In Python-land, you don't have to
> do this.

Having to inspect library code in language A to import into language B
does not make language A a better language for writing library code.
It merely means that language A happens to have one more library of
useful code for a given problem domain. Or, to borrow your words, it
does not follow that language B becomes "particularly bad at" writing
"glue" code.

taltman@noshpam.lbl.government

2004-03-27, 12:24 am

David Van Horn <dvanhorn@cs.uvm.edu> writes:

> taltman@noshpam.lbl.government wrote:
>
> SRFI 49 provides exactly this extension.

Wow! Thanks for bringing this to my attention. Aside from support, I
don't think I have had nearly enough FORTRAN or Python experience
under my belt to give meaningful commentary. :-)

~Tomer

--
()

taltman@noshpam.lbl.government

2004-03-27, 12:24 am

Alan Shutko <ats@acm.org> writes:

> taltman@noshpam.lbl.government writes:
>
>
> A huge part of the problem is that few bioinformaticists are actually
> good programmers. A compiler won't help speed up an algorithm that

This is somewhat true. In the lab that I work in, there are all types:
* CS types learning biology
* bio types learning CS
* wizards who can hold their own in both fields.

The one thing that they share is Perl as a crutch. This is due to
cultural and historical reasons...

> uses 1GB to load a small 23MB sequence. They will patch five things
> from CPAN haphazardly together and wonder why it's so slow and takes
> too much memory. Why? Because each piece they took was designed to
> do something else.... Even the big names aren't immune to this
> problem.

Very true.

~Tomer

>
> --
> Alan Shutko <ats@acm.org> - I am the rocks.
>

--
()

taltman@noshpam.lbl.government

2004-03-27, 12:24 am

Ray Dillinger <bear@sonic.net> writes:

> Alan Shutko wrote:
>
> You describe a common pattern of naive programming, which is called
> exponential abstraction.
>

[snnnniiipppp]

>
> Anyway; -- if most Bioinformatics code is currently suffering from
> exponential abstraction, then there's an opportunity to provide much
> better code than they're using now. But I'm not familiar enough with
> the field to know what the code would need to do or what the scope of
> the programming projects would be. How may I become more enlightened
> as to the problems that need solved there?

Here's the skinny:

Bioinformaticists work in a heterogeneous software environment, but a
lot of the computational work gets done in:

* Matlab
* Perl
* GNU R (statistical calculation interpreter)

So, if you're using Perl, then the first place you should look is:

* bioperl.org

This is a site which sponsors "bio" + (fill in the blank) + ".org"
development efforts:

* bioinformatics.org

A lot of the work is in data curation and integration, so that
meaningful calculations can be done of the system behavior.

I work with a group that's developing DARPA BioSPICE, and their work
is geared towards that very thing. Yes, it is
modeled after the celebrated SPICE analysis package. The key insight
here for the non-bio minded, is that the cell is nothing more than a
noisy, stochastic, analog, nonlinear system. :-)

www.biospice.org

Whew! I have lots more to say, but that's it for now.

~Tomer

>
> Bear

--
()

taltman@noshpam.lbl.government

2004-03-27, 12:24 am

taltman@noshpam.lbl.government

2004-03-27, 12:24 am

ix@io.com (Lupo LeBoucher) writes:

[snip]

> Actually, given Lisp and some Norvig books (and some "glue" code), one
> could do truely astounding things in Bioinformatics.

If you have something in mind, please; give, give!

As for good glue code, Scheme/Lisp can do the job.

>
> I have a couple of scientist friends at a to-remain-nameless local
> bioinformatics company. They end up using Matlab (*eeeeeeeeeeewww*), talking
> to SQL, doing pattern matching and Bayesian network type stuff on big
> data sets. If they have a need to go fast, if you can imagine this, they
> send it to their in-house code monkeys who reimplement the work in VISUAL
> FOOKIN BASIC. This is one of the top biosciences companies in the known
> universe, mind you. Presumably, they choose their code-monkeys based on
> ready availability rather than actual competence. You could probably
> replace their whole department with two guys and a Lisp. You could also
> probably build some really neat code for them which they would pay for, if
> you sat down and talked to some of them.

I see two ideas here, neither which is fully developed:
* use Lisp to do things in Bioinformatics which are otherwise
hard/impossible.
* speed up existing development tools.

Could you elaborate?

> them some kind of FEMLISP derivative which has all the bells and whistles

At first, I thought you were referring to some sort of gender-specific
implementation. :-}

> Beyond that, as I recall from an examination of the CLISP source tree, the
> authors of CLISP are interested in financial analysis and derivatives type
> trading. That's the biggest pipe of money in the world, and they use
> fairly naieve methods.

There's a guy at my lab who started out in theoretical physics in
Russia, moved to NY, started in Burger King while learning English,
worked for years as a Technical Analyst for some high finance firm,
and now is "retired" as a post-doc. :-) So I know that the good
technical analysis group of a financial research department actually
use some very sophisticated methods.

> At some point I will come eat food with the other Bay Area lispers, if you
> promise not to make me foot the bill for my dislike of emacs and
> defsystem.

What's the saying? 'Hit the philistines three times on the head with
the Elisp Manual.' ;-)

~Tomer

>
> -Lupo <ix@pentagon.io.com>
> "Java: the elegant simplicity of C++ and the blazing speed of Smalltalk"
>

--
()

taltman@noshpam.lbl.government

2004-03-27, 12:24 am

taltman@noshpam.lbl.government

2004-03-27, 12:24 am

tfb@famine.OCF.Berkeley.EDU (Thomas F. Burdick) writes:

> ix@io.com (Lupo LeBoucher) writes:
>
>
> Ha ha ha! Oh, you weren't kidding? Uhm, try adding a bunch of
> biological knowledge to that. The days of being able to get anything
> from a naive/ignorant application of CS to biology are over. We need
> bioinformaticians who are *both* biologists and computer scientists.
> Either one alone won't cut it, at least if you're looking for serious
> progress.

Well, I wouldn't be so quick on that. I think that there are still
many untapped methods/theories/algorithms/approaches in biology and
computer science which can be matched with problems in either field to
yield progress. But you're right: the obvious ones have already been
explored, and further development along these tracks require someone
with a solid grounding in both fields.

As I alluded to in another post, the key here is integration:

* integrate the data (bioDBMS' are a huge area of research)
* integrate the tools (allow all those theoretical tools to interoperate)
* agree on representation standards ( XML friendly )

There are already some platforms which are allowing this in a nascent
form:

BioCYC (implemented in LISP!)
www.biocyc.org

BioSPICE:
www.biospice.org

The Systems Biology Workbench:
www.sbw-sbml.org

I'm not done yet, but that's it for now!

~Tomer

>
> --
> /|_ .----------------------.
> ,' .\ / | No to Imperative war |
> ,--' _,' | Wage cons war! |
> / / `----------------------'
> ( -. |
> | ) |
> (`-. '--.)
> `. )----'

;-)

--
()

taltman@noshpam.lbl.government

2004-03-27, 12:24 am

tfb@famine.OCF.Berkeley.EDU (Thomas F. Burdick) writes:

> ix@io.com (Lupo LeBoucher) writes:
>
>
> Ha ha ha! Oh, you weren't kidding? Uhm, try adding a bunch of
> biological knowledge to that. The days of being able to get anything
> from a naive/ignorant application of CS to biology are over. We need
> bioinformaticians who are *both* biologists and computer scientists.
> Either one alone won't cut it, at least if you're looking for serious
> progress.

Well, I wouldn't be so quick on that. I think that there are still
many untapped methods/theories/algorithms/approaches in biology and
computer science which can be matched with problems in either field to
yield progress. But you're right: the obvious ones have already been
explored, and further development along these tracks require someone
with a solid grounding in both fields.

As I alluded to in another post, the key here is integration:

* integrate the data (bioDBMS's' are a huge area of research)
* integrate the tools (allow all those theoretical tools to interoperate)
* agree on representation standards ( XML friendly )

There are already some platforms which are allowing this in a nascent
form:

BioCYC (implemented in LISP!)
www.biocyc.org

BioSPICE:
www.biospice.org

The Systems Biology Workbench:
www.sbw-sbml.org

I'm not done yet, but that's it for now!

~Tomer

>
> --
> /|_ .----------------------.
> ,' .\ / | No to Imperative war |
> ,--' _,' | Wage cons war! |
> / / `----------------------'
> ( -. |
> | ) |
> (`-. '--.)
> `. )----'

;-)

--
()

taltman@noshpam.lbl.government

2004-03-27, 12:24 am

Chris Hall <hall.cj@verizon.net> writes:

> To develop a real-world bioinformatics app in anything approaching a
> rapid or responsive way with any real chance of success would seem to
> require at least some of this sort of 'pair programming'. Best of
> luck!

I agree with you 100% on this. And this is how expert systems
programming should be done. Wait, am I suggesting something? :-)

~Tomer

>
> I just *love* putting computers to work for people. Sigh. :-D
>
> + CJHall
>
> --
> Democracy: The worship of jackals by jackasses.
> -- H.L. Mencken

--
()

taltman@noshpam.lbl.government

2004-03-27, 12:24 am

ix@io.com (Lupo LeBoucher) writes:

> As for actually making money doing this sort of thing (which is the
> subject of this discussion), there is certainly plenty of room for CS
> people to do so without knowing a thing about biology, as I have already
> pointed out.

I agree with you in principle, but I'm still missing the
details. Could you elaborate?

~Tomer

>
> -Lupo
> 'Sex is the mysticism of materialism.'-Malcolm Muggeridge <ix@io.com>

--
()

taltman@noshpam.lbl.government

2004-03-27, 12:24 am

taltman@noshpam.lbl.government

2004-03-27, 12:24 am

dave_a_fisher@yahoo.com (David Fisher) writes:

> taltman@noshpam.lbl.government wrote in message news:<4pkptbj84ai.fsf@thar.lbl.gov>...
>
> What bioinformatics are you talking about, specifically? Most
> bioinformatics seems to be either some trivial stuff: accessing online
> databases, parsing of their internal formats, saving data to disk,
> serving data to client apps, for which Perl is a semi-reasonable

Well, you can say this statement about *anything*; bioinformatics,
finance, accounting, etc. The key is understanding the domain, and the
paradigms there that people work around. For bioinformaticists, the Central
Dogma of Molecular Biology is:

DNA -> RNA -> protein

All else is details. :-)

Make that easy, and you're moving in the right direction.

> solution; or it's high-performance stuff like sequence analysis. Some
> do abuse Perl and use it for the performance-demanding tasks, but it's
> only because they truly believe Perl is as good as it gets, or they
> are just lazy or too busy to learn another language. So yes, if you

Both of what you say are true. A combination of historical and
cultural forces. I'll elaborate if desired.

> can compile *Perl* to something that would run very fast, there is a
> gold mine there, and that's probably an understatement. But if you
> want to sell *new* VHLL to bioinformaticians, I'd be a bit sceptical.

I agree. That's my general feeling.

>
>
> Open source on top of open source, and you want to charge money for
> the result, essentially for the packaging, like Redhat now does. Did I
> understand your idea correctly?

Well, I never claimed that this was my money-making scheme; I only
think that this compiler project would work if it were
proprietary ( and I'm surprised that no one has done it till now
). But I prefer to work in open-source...

~Tomer

--
()

taltman@noshpam.lbl.government

2004-03-27, 12:24 am

taltman@noshpam.lbl.government

2004-03-27, 12:24 am

Feuer <feuer@his.com> writes:

> David Fisher wrote:
>
>
> Packaging? What about training?

Lisp-Certified Bioinformaticist? :-)

Seriously, though. You need quite a rep (Cisco, Oracle, Microsoft,
Sun) to put out your own certification...

~Tomer

>
> David

--
()

taltman@noshpam.lbl.government

2004-03-27, 12:24 am

Xref: kermit comp.lang.lisp:128045 comp.lang.scheme:40407

Feuer <feuer@his.com> writes:

> David Fisher wrote:
>
>
> Packaging? What about training?

Lisp-Certified Bioinformaticist? :-)

Seriously, though. You need quite a rep (Cisco, Oracle, Microsoft,
Sun) to put out your own certification...

~Tomer

>
> David

--
()

Feuer

2004-03-27, 12:24 am

taltman@noshpam.lbl.government wrote:

> Feuer <feuer@his.com> writes:
>
>
>
>
> Lisp-Certified Bioinformaticist? :-)
>
> Seriously, though. You need quite a rep (Cisco, Oracle, Microsoft,
> Sun) to put out your own certification...

Not talking about certifications. I'm talking about training people to
use Lisp and Lisp software to work more efficiently within their
particular field.

David

Thomas F. Burdick

2004-03-27, 12:25 am

ix@io.com (Lupo LeBoucher) writes:

> In article <xcvfzcd5emw.fsf@famine.OCF.Berkeley.EDU>,
> Thomas F. Burdick <tfb@famine.OCF.Berkeley.EDU> wrote:
>
> The guys I know who do this sort of thing are all physicists, and they
> seem to get a lot of research done without knowing much CS or biology.
> They seem to bring a rather different and useful skillset to the plate
> than biologists or CS types do. Perhaps because they're used to applying
> mathematical ideas to, like, reality.

Wow, so are biologists. And this is irrelevant, weren't you just
talking about computer scientists with no science training a second ago?

> As for actually making money doing this sort of thing (which is the
> subject of this discussion), there is certainly plenty of room for CS
> people to do so without knowing a thing about biology, as I have already
> pointed out.

Wow, I see your expert debating techniques are back at work. This
pretty much amounts to a long-winded, "uh-huh, can too." You didn't
point anything out, you asserted it. "Pointing something out" implies
that you had anything to back you up.

--
/|_ .-----------------------.
,' .\ / | No to Imperialist war |
,--' _,' | Wage class war! |
/ / `-----------------------'
( -. |
| ) |
(`-. '--.)
`. )----'

Thomas F. Burdick

2004-03-27, 12:25 am

taltman@noshpam.lbl.government writes:

> tfb@famine.OCF.Berkeley.EDU (Thomas F. Burdick) writes:
>
>
> Well, I wouldn't be so quick on that. I think that there are still
> many untapped methods/theories/algorithms/approaches in biology and
> computer science which can be matched with problems in either field to
> yield progress. But you're right: the obvious ones have already been
> explored, and further development along these tracks require someone
> with a solid grounding in both fields.

I suspect that part of the reason that some CS folks think that they
don't need a good biological grounding is because they don't have one,
so they don't know much of the sordid history of the unthinking
application of analytical techniques to biological problems. It seems
to be particularly easy to find somewhat convincing mathematical
artifacts in biological systems. At this point in history, I think
it's safe to say that if you can't make a strong materialist argument
as to why it makes sense to apply some analytical technique to some
biological problem, odds are you're going to do more harm than good.

> As I alluded to in another post, the key here is integration:
>
> * integrate the data (bioDBMS' are a huge area of research)
> * integrate the tools (allow all those theoretical tools to interoperate)

No doubt. An unfortunate amount of programmer time goes into gluing
things together that should have fit in the first place.

> * agree on representation standards ( XML friendly )

Yuck, but yeah, XML is probably going to be the necessary backbone here.

--
/|_ .-----------------------.
,' .\ / | No to Imperialist war |
,--' _,' | Wage class war! |
/ / `-----------------------'
( -. |
| ) |
(`-. '--.)
`. )----'

taltman@noshpam.lbl.government

2004-03-27, 12:25 am

tfb@famine.OCF.Berkeley.EDU (Thomas F. Burdick) writes:

[snip]

> I suspect that part of the reason that some CS folks think that they
> don't need a good biological grounding is because they don't have one,
> so they don't know much of the sordid history of the unthinking
> application of analytical techniques to biological problems. It seems

Well, my experience in my lab at least has been with the computer
scientists being intimidated out of their mind. And vice-versa for
biologists having to code. Everyone in our lab feels inadequate,
because they have to work with co-workers who are experts in a
different field than what they studied. So everyone's learning
something different.

> to be particularly easy to find somewhat convincing mathematical
> artifacts in biological systems. At this point in history, I think
> it's safe to say that if you can't make a strong materialist argument
> as to why it makes sense to apply some analytical technique to some
> biological problem, odds are you're going to do more harm than good.

True, it should be only applied when it can be justified. My
hypothesis is that there is a lot of potential areas of such application.

>
>
> No doubt. An unfortunate amount of programmer time goes into gluing
> things together that should have fit in the first place.
>
>
> Yuck, but yeah, XML is probably going to be the necessary backbone here.

Well, if we can't get the heathens to s-exprs, then XML is better than
nothing... :-)

~Tomer

>
> --
> /|_ .----------------------.
> ,' .\ / | No to Imperative war |
> ,--' _,' | Wage cons war! |
> / / `----------------------'
> ( -. |
> | ) |
> (`-. '--.)
> `. )----'

--
()

taltman@noshpam.lbl.government

2004-03-27, 12:25 am

Feuer <feuer@his.com> writes:
> Not talking about certifications. I'm talking about training people
> to use Lisp and Lisp software to work more efficiently within their
> particular field.

Sorry about the certification/training mixup.

Well, I can imagine this kind of 'service' as being a part of a
business plan. But I'm skeptical about people using Lisp
directly. Under the hood and on the server, sure. They'll never
know. Or it can be used "through the backdoor" as with Emacs and
AutoCAD, where lisp is used to make the tool more useful and
automated.

What do you think?

~Tomer

>
> David

--
()

Ng Pheng Siong

2004-03-27, 12:25 am

According to <taltman@noshpam.lbl.government>:
> Well, my experience in my lab at least has been with the computer
> scientists being intimidated out of their mind. And vice-versa for
> biologists having to code. Everyone in our lab feels inadequate,
> because they have to work with co-workers who are experts in a
> different field than what they studied. So everyone's learning
> something different.

"Being intimidated" == "fearful of being found out"?

I don't believe an expert in any particular field will be intimated by an
expert in another field when they have to work together. Each will learn to
trust the judgement of the other.

Not talking about your lab specifically, mind.

Cheers.

--
Ng Pheng Siong <ngps@netmemetic.com>

http://firewall.rulemaker.net -+- Firewall Change Management & Version Control
http://sandbox.rulemaker.net/ngps -+- Open Source Python Crypto & SSL

David Steuber

2004-03-27, 12:25 am

taltman@noshpam.lbl.government writes:

> Well, my experience in my lab at least has been with the computer
> scientists being intimidated out of their mind. And vice-versa for
> biologists having to code. Everyone in our lab feels inadequate,
> because they have to work with co-workers who are experts in a
> different field than what they studied. So everyone's learning
> something different.

That actually sounds like a fun place to work.

--
Those who do not remember the history of Lisp are doomed to repeat it,
badly.

> (dwim x)
NIL

taltman@noshpam.lbl.government

2004-03-27, 12:25 am

ngps@netmemetic.com (Ng Pheng Siong) writes:

> According to <taltman@noshpam.lbl.government>:
>
> "Being intimidated" == "fearful of being found out"?
>
> I don't believe an expert in any particular field will be intimated by an
> expert in another field when they have to work together. Each will learn to
> trust the judgement of the other.

Well, since our lab throws together physics, biology, chemistry,
computer science, and statistics, there's a lot of basics for a
new-come'er to pick up to get the gist of others' research. Just a
steep learning curve, for post-docs & grad students used to being in a
much more homogeneous environment.

> Not talking about your lab specifically, mind.

Dutifully noted, ;-)

~Tomer

>
> Cheers.
>
> --
> Ng Pheng Siong <ngps@netmemetic.com>
>
> http://firewall.rulemaker.net -+- Firewall Change Management & Version Control
> http://sandbox.rulemaker.net/ngps -+- Open Source Python Crypto & SSL

--
()

David Fisher

2004-03-27, 12:25 am

taltman@noshpam.lbl.government wrote in message news:<4pkptbj84ai.fsf@thar.lbl.gov>...
>
> Well, here's a "vertical/horizontal" that I'm surprised hasn't been
> exploited:
>
> Scheme/Lisp has fantastic (meta)linguistic capabilities. One thing
> that I could imagine would be taking VHLLs which are common in
> industry, and building compilers for them by first 'compiling' them to
> Lisp/Scheme.
>
> When I see how addicted bioinformaticists are to Perl, for example, I
> see a gold mine of opportunity. If you could offer them a compiler for
> a VHLL language that they use,

What bioinformatics are you talking about, specifically? Most
bioinformatics seems to be either some trivial stuff: accessing online
databases, parsing of their internal formats, saving data to disk,
serving data to client apps, for which Perl is a semi-reasonable
solution; or it's high-performance stuff like sequence analysis. Some
do abuse Perl and use it for the performance-demanding tasks, but it's
only because they truly believe Perl is as good as it gets, or they
are just lazy or too busy to learn another language. So yes, if you
can compile *Perl* to something that would run very fast, there is a
gold mine there, and that's probably an understatement. But if you
want to sell *new* VHLL to bioinformaticians, I'd be a bit sceptical.

> to speed up the Gigabytes of genetic
> data that they spend *w

s* chugging through with Perl, I'm confident
> that they'd use that compiler.
>
> Just my $0.02,
>
> ~Tomer
>
> P.S.- I think that a package for Scsh, which gives the user the
> ability to not use parens (like the "Sugar" package), would be a great
> replacement for Perl, IMNSHO ( I know, I know, in my dreams... ).

Open source on top of open source, and you want to charge money for
the result, essentially for the packaging, like Redhat now does. Did I
understand your idea correctly?

Lupo LeBoucher

2004-03-27, 12:25 am

In article <xcv65d35nxf.fsf@famine.OCF.Berkeley.EDU>,
Thomas F. Burdick <tfb@famine.OCF.Berkeley.EDU> wrote:
>ix@io.com (Lupo LeBoucher) writes:
>
>
>Wow, so are biologists.

Typically, not, really. Which is why there are all manner of fellowships
devoted to converting hard scientists into biologists who know math. It's
also why so many Nobel prizes in biology go to people with physics and
chemistry training. This seems to be changing somewhat, but relatively slowly.

> And this is irrelevant, weren't you just
>talking about computer scientists with no science training a second ago?

I dunno man; you brought it up.

>
>Wow, I see your expert debating techniques are back at work. This
>pretty much amounts to a long-winded, "uh-huh, can too." You didn't
>point anything out, you asserted it. "Pointing something out" implies
>that you had anything to back you up.

*snork*
You really got a chip on your shoulder, dontcha?
What's the matter; did brother Lupo piss in your beer?

I have already pointed out several specific ways in which Lispey CS people
can make money in Bioinformatics-land, and in a specific large company in
the Bay Area, even. Viz; you could vastly outpace the productivity of the
crew of Visual Basic weenies who do their "production code" and you could
do a lot better than the crap available in Matlab packages at pattern
matching and Baysean searches and fancy database queries by sitting down
with Lisp and some Norvig books. Just organizing the database queries in a
clever way is probably a marketable product.

I've also pointed out two areas in government contracting one could make
some money using Lisp. I've been specific enough, if you know how to run a
search engine, you can figure out what the damned grant numbers are (or,
you could just ask me).

You have sneered a little, which is entertaining, but it isn't much of a
contribution to the discussion, now is it?

-Lupo
"The earth has people of two kinds: The ones who think have no religion,
the others do and have no minds." -Abu al-Ala al Maarri, 11th century poet
<ix@io.com>

Lupo LeBoucher

2004-03-27, 12:25 am

In article <ouyoeqxl7vf.fsf@panix3.panix.com>,
Carl Shapiro <cshapiro+spam@panix.com> wrote:
>ix@io.com (Lupo LeBoucher) writes:
>
>
>Having to inspect library code in language A to import into language B
>does not make language A a better language for writing library code.
>It merely means that language A happens to have one more library of
>useful code for a given problem domain. Or, to borrow your words, it
>does not follow that language B becomes "particularly bad at" writing
>"glue" code.

Um, yeah; in an ideal world, someone would take CPAN and shoe-horn it into
CMU-CL (or even just shoe-horn the basic functionality of Perl itself
into Lisp, like Graham is trying to do with Arc), and that could make a
Lisp which is far more handy for "glue" code than Perl is, but nobody has
done that, so we're stuck with shitty scripting languages for day to day
work, or reimplementing language A in language B.

Not many people get paid to reimplement language A in language B once we
get out of grad school. And it shows.

-Lupo
"it is at once, a theater of the absurd, a decomposing corpse, and an
insane asylum."-former UN ambas

or Pat Moynihan on the UN <ix@io.com>

Michele Simionato

2004-03-27, 12:25 am

ix@io.com (Lupo LeBoucher) wrote in message news:<XLydndr_huRSosvd4p2dnA@io.com>...
> The guys I know who do this sort of thing are all physicists, and they
> seem to get a lot of research done without knowing much CS or biology.
> They seem to bring a rather different and useful skillset to the plate
> than biologists or CS types do. Perhaps because they're used to applying
> mathematical ideas to, like, reality.

Uhmm ... I cannot resist the temptation to quote Joseph Likken:

Physicists used to be smarter and more arrogant than biologist;
now, we are just smarter. -- Joseph Likken, DPF 2000 Ohio State University

Rob Warnock

2004-03-27, 12:25 am

Lupo LeBoucher <ix@io.com> wrote:
+---------------
| Um, yeah; in an ideal world, someone would take CPAN and shoe-horn it into
| CMU-CL (or even just shoe-horn the basic functionality of Perl itself
| into Lisp, like Graham is trying to do with Arc), and that could make a
| Lisp which is far more handy for "glue" code than Perl is, but nobody has
| done that, so we're stuck with shitty scripting languages for day to day
| work, or reimplementing language A in language B.
+---------------

Well, just because CL isn't *perfect* for scripting doesn't mean it's
not awfully darned useful!! I use CMUCL for scripting lots of stuff.
Some recent examples:

"date-nist" -- fetches the current time from (one or more of)
the NIST time server(s). The heart of it is this function:

(defun fetch-time/rfc868 (host)
(let* ((fd (connect-to-inet-socket host 37))
(stream (system:make-fd-stream
fd
:element-type '(unsigned-byte 8)
:buffering :none)))
(with-open-stream (s stream)
(loop repeat 4 ; [Thanks, Erik!]
for time = (read-byte s)
then (+ (read-byte s) (* time 256))
finally (return time)))))

"csv_to_html" -- Convert a CSV (Comma-Separated Variables) file into
an HTML table. The heart of it is this function:

;;; PARSE-CSV-LINE -- Parse one CSV line into a list of fields,
;;; stripping quotes and field-internal escape characters.
;;; Lexical states: NORMAL QUOTED ESCAPED QUOTED+ESCAPED
;;;
(defun parse-csv-line (line)
(when (or (string= line "") ; special-case blank lines
(char= #\# (char line 0))) ; or those starting with "#"
(return-from parse-csv-line '()))
(loop for c across line
with state = 'normal
and results = '()
and chars = '() do
(ecase state
((normal)
(case c
((#\") (setq state 'quoted))
((#\\) (setq state 'escaped))
((#\,)
(push (coerce (nreverse chars) 'string) results)
(setq chars '()))
(t (push c chars))))
((quoted)
(case c
((#\") (setq state 'normal))
((#\\) (setq state 'quoted+escaped))
(t (push c chars))))
((escaped) (push c chars) (setq state 'normal))
((quoted+escaped) (push c chars) (setq state 'quoted)))
finally
(progn
;; close still-open field
(push (coerce (nreverse chars) 'string) results)
(return (nreverse results)))))

"keto" -- Given a number of grams of protein, carbohydrate, and fat,
show the total number of calories and the "ketogenic ratio" [useful
to those on low-carb diets]:

% cat ~/bin/keto
#!/usr/local/bin/cmucl -script
(cond
((= 3 (length *script-args*))
(destructuring-bind (p c f)
(mapcar #'read-from-string *script-args*)
(format t "grams: protein ~a carb ~a fat ~a~%" p c f)
(format t "ketogenic ratio: ~a~%"
(/ (+ (* 0.9 f) (* 0.46 p))
(+ (* 1.0 c) (* 0.1 f) (* 0.58 p))))
(format t "total calories: ~a~%"
(+ (* 4 p) (* 4 c) (* 9 f)))))
(t
(format t "usage: ~a <protein> <carb> <fat>~%" *script-name*)
(format t "(enter all amounts in grams)~%")
(quit 1)))
% keto.cl 8 6 17
grams: protein 8 carb 6 fat 17
ketogenic ratio: 1.5380875
total calories: 209
%

"sum-time-user-sys" -- Do some trivial processing on the output of the
"time" builtin command in "csh". [Shown in a previous post today.]

"random" -- Generate random strings which are legal as URLs, filenames,
and passwords on most systems, thus shell and URL metacharacters
must be excluded. Takes the time of day plus a number of bytes from
"/dev/urandom" and uses it to seed the CMUCL MT19937 random number
generator, then crank that some number of times and encode the output
into acceptable text [6 bits per character] of the desired length
[default 16]:

% random
WhiTrVcHUQw8XavI
% random 64
BbnmXL4Jk_j_2kFF@8R4nYbiqtH@esAY0z2FbDug
x3yRKRp_aetqNzbh6EtoUG2w
% repeat 3 random
z0P0xuFm6rKBosee
W0d_BWBiVZIkQvg2
LJUHkFRrhfictQRv
% repeat 5 random 8
kPIbakFj
6T0KvOB4
2GINrD3S
D39TQIV3
1vjJ8KzQ
%

"wild" -- Construct more complex wild-card command than are natively
convenient in Unix shell, e.g., the sort of thing TOPS-10 used to
let you do, stuff like "ren *.foo *.bar" [which does *not* do the
same thing at all in Unix!!]. It's just a loop around CL's DIRECTORY
and TRANSLATE-PATHNAME and a FORMAT to print it all. It doesn't do
the commands itself, it just outputs them, but if you like what you
see then, you can repeat it and pipe the output to "/bin/sh -x" to
execute them (the "-x" lets you see what's going on). Example:

% ls -l foo1*
-rwxr-xr-x 1 rpw3 rpw3 2099 Feb 6 03:52 foo1
-rw-r--r-- 1 rpw3 rpw3 223 Feb 6 03:48 foo1.lisp
-rw-r--r-- 1 rpw3 rpw3 882 Feb 6 03:52 foo1.x86f
% wild
usage: wild command pattern [ repl-patterns... ]
% wild mv foo1\* bar2\*
mv foo1 bar2
mv foo1.lisp bar2.lisp
mv foo1.x86f bar2.x86f
% !! | sh -x
wild mv foo1\* bar2\* | sh -x
+ mv foo1 bar2
+ mv foo1.lisp bar2.lisp
+ mv foo1.x86f bar2.x86f
% ls -l bar2*
-rwxr-xr-x 1 rpw3 rpw3 2099 Feb 6 03:52 bar2
-rw-r--r-- 1 rpw3 rpw3 223 Feb 6 03:48 bar2.lisp
-rw-r--r-- 1 rpw3 rpw3 882 Feb 6 03:52 bar2.x86f
%

Lest I bore people [if I haven't already!], I'll stop there. But suffice
it to say that the more I use CL and become familiar with various nuances,
the more I use it *instead* of scripts in "sh" or Perl (as well as in
conjunction with them).

-Rob

-----
Rob Warnock <rpw3@rpw3.org>
627 26th Avenue <URL:http://rpw3.org/>
San Mateo, CA 94403 (650)572-2607

Björn Lindberg

2004-03-27, 12:25 am

ix@io.com (Lupo LeBoucher) writes:

> In article <xcv65d35nxf.fsf@famine.OCF.Berkeley.EDU>,
> Thomas F. Burdick <tfb@famine.OCF.Berkeley.EDU> wrote:
>
> Typically, not, really. Which is why there are all manner of fellowships
> devoted to converting hard scientists into biologists who know math. It's
> also why so many Nobel prizes in biology go to people with physics and
> chemistry training. This seems to be changing somewhat, but relatively slowly.

Except that there isn't a Nobel Prize in biology.

Björn

Scott Schwartz

2004-03-31, 6:46 pm

rpw3@rpw3.org (Rob Warnock) writes:
> % cat ~/bin/keto
> #!/usr/local/bin/cmucl -script

You forgot to include the code to handle exceptions, disable the
debugger, defang read-eval, keep garbage from going to stdout, keep
stdin away from random repls, convincing it that end of file means to
stop reading and not to go for /dev/tty instead, etc.

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